You are doing it wrong at all. Don't put anything in base.
You suppose to load all other mods assets using "fs_extraGames" cvar on startup. Just modify start_jaMME.cmd with any text editor and replace "japlus japp" with "RPMod" or whatever the mod folder called. Or make your custom start_jaMME_RPMod.cmd.
I guess your issues may happen because it mixes anims from ja+ mod and rpmod.
If my solution doesn't help, then send demos, give a download link for the mod and tell me what2do to reproduce your problems.
I need their numbers anyways.